DB code: S00022

RLCP classification 1.15.8240.2170 : Hydrolysis
CATH domain 1.10.575.10 : P1 Nuclease Catalytic domain
CSA 1ak0
M-CSA 1ak0

CATH domain Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P24289 Nuclease P1
Endonuclease P1
Deoxyribonuclease P1
PF02265 (S1-P1_nuclease)
[Graphical View]

KEGG enzyme name
Aspergillus nuclease S1
endonuclease S1 (Aspergillus)
single-stranded-nucleate endonuclease
deoxyribonuclease S1
deoxyribonuclease S1
nuclease S1
Neurospora crassa single-strand specific endonuclease
S1 nuclease
single-strand endodeoxyribonuclease
single-stranded DNA specific endonuclease
single-strand-specific endodeoxyribonuclease
single strand-specific DNase
Aspergillus oryzae S1 nuclease

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P24289 NUP1_PENCI Endonucleolytic cleavage to 5''- phosphomononucleotide and 5''-phosphooligonucleotide end-products. Secreted. Binds 3 zinc ions.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00046 C00039 C00001 C00171 C00351
Compound Zinc RNA DNA H2O 5'-Phosphomononucleotide 5'-Phosphooligonucleotide
Type heavy metal nucleic acids nucleic acids H2O nucleotide nucleic acids,phosphate group/phosphate ion
ChEBI 29105
PubChem 32051
1ak0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:3x_ZN Unbound Unbound Analogue:ADS-THS-THS-THS Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P24289 & literature [2]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ak0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 45;ARG 48 TRP 1;HIS 6(Zinc3 binding);ASP 45;HIS 60;HIS 116(Zinc1 binding);ASP 120(Zinc1 & Zinc2 binding);HIS 126;HIS 149;ASP 153(Zinc2 binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
p.421-423, Fig.6

Medline ID
PubMed ID 1710977
Journal EMBO J
Year 1991
Volume 10
Pages 1607-18
Authors Volbeda A, Lahm A, Sakiyama F, Suck D
Title Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.
Related PDB
Related UniProtKB P24289
Medline ID
PubMed ID 9726413
Journal Proteins
Year 1998
Volume 32
Pages 414-24
Authors Romier C, Dominguez R, Lahm A, Dahl O, Suck D
Title Recognition of single-stranded DNA by nuclease P1: high resolution crystal structures of complexes with substrate analogs.
Related PDB 1ak0
Related UniProtKB P24289
Medline ID
PubMed ID 10563833
Journal Chem Res Toxicol
Year 1999
Volume 12
Pages 1077-82
Authors Wang Y, Taylor JS, Gross ML
Title Nuclease P1 digestion combined with tandem mass spectrometry for the structure determination of DNA photoproducts.
Related PDB
Related UniProtKB

According to the literature [2], the hydrolytic reaction, where a water is activated by cofactor zinc ion, proceeds as follows:
(1) A water molecule, which is bridging cofactors, Zinc1 and Zinc3, is activated to make a hydroxide ion. This activation is assisted by Asp45, which is also ligating zinc1.
(2) The activated water makes a nucleophilic attack on the phosphorus atom of the scissile phosphoric ester bond, in line with the P-O3' bond. (This attack will lead to the inversion of the phosphate, suggsting an SN2-like reaction.)
(3) The pentacovalent transition state is stabilized by Zinc2 and Arg48.
(4) Finally, the P-O3' bond will be cleaved.

Created Updated
2004-03-19 2009-03-11